This invention relates to in vitro diagnostic detection of pathogenic bacteria, and specifically relates to compositions and assays for detecting many species of Mycobacterium by using in vitro nucleic acid amplification and detection of amplified products.
Detection of Mycobacterium species in clinical species is important as a clinical diagnostic tool. Historically, M. tuberculosis was thought to be the only clinically significant pathogen in this genus. A rise in the incidence of drug-resistant strains of M. tuberculosis has further emphasized the need to detect this species. Other Mycobacterium species, however, are also clinically important. These are sometimes referred to as xe2x80x9cMOTTxe2x80x9d for Mycobacterium other than tuberculosis, commonly including M. avium/intracellulare complex organisms (M. avium, M. intracellulare, M. paratuberculosis, commonly referred to as MAIC), M. gordonae, M. fortuitum, M. chelonae, M. mucogenicum and mixtures of Mycobacterium species in a clinical specimen. For example, fast-growing opportunistic infections by M. avium complex (MAC) bacteria have been shown to occur frequently in AIDS and other immunocompromised individuals. In such infected individuals, at least 106 MAC cells/ml of sputum sediment have been found. Therefore, detection assays that can detect, and optimally distinguish between, many species of Mycobacterium are clinically important.
Many clinical methods for detecting and identifying Mycobacterium species in samples require analysis of the bacteria""s physical characteristics (e.g., acid-fast staining and microscopic detection of bacilli), physiological characteristics (e.g., growth on defined media) or biochemical characteristics (e.g., membrane lipid composition). These methods require relatively high concentrations of bacteria in the sample to be detected, may be subjective depending on the clinical technician""s experience and expertise, and are time-consuming. Because Mycobacterium species are often difficult to grow in vitro and may take several weeks to reach a useful density in culture, these methods can also result in delayed patient treatment and costs associated with isolating an infected individual until the diagnosis is completed.
More recently, assays that detect the presence of nucleic acid derived from bacteria in the sample have been preferred because of the sensitivity and relative speed of the assays. In particular, assays that use in vitro nucleic acid amplification of nucleic acids present in a clinical sample can provide increased sensitivity and specificity of detection. Such assays, however, can be limited to detecting one or a few Mycobacterium species depending on the sequences amplified and/or detected.
Assays and reagents for detecting Mycobacterium nucleic acid sequences have been previously disclosed, for example, in U.S. Pat. Nos. 5,554,516, 5,766,849, 5,906,917, 5,908,744; European Patent Nos. EP 0528306 and EP 0818465; and published PCT Patent Applications WO 9636733 and WO 9723618.
The present invention provides compositions and relatively simple diagnostic methods that detect a wide spectrum of Mycobacterium species that may be present in a clinical sample.
According to one aspect of the invention, there is provided a method of detecting Mycobacterium species present in a biological sample, comprising the steps of providing a biological sample containing nucleic acid from at least one Mycobacterium species comprising a Mycobacterium 16S ribosomal RNA (rRNA) or DNA encoding 16S rRNA; amplifying the Mycobacterium 16S rRNA or DNA in an in vitro nucleic acid amplification mixture comprising at least one polymerase activity, and at least two primers having sequences selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:34, SEQ ID NO:37 and SEQ ID NO:38 to produce amplified Mycobacterium nucleic acid; and detecting the amplified Mycobacterium nucleic acid by detecting a label associated with the amplified Mycobacterium nucleic acid. One embodiment of the method further comprises the steps of adding to the biological sample at least one capture oligonucleotide that specifically hybridizes to the Mycobacterium 16S rRNA and an immobilized nucleic acid that hybridizes to the capture oligonucleotide under hybridizing conditions to produce a hybridization complex; and separating the hybridization complex from other components of the biological sample before the amplifying step. In one embodiment, the amplifying step amplifies 16S rRNA or DNA encoding 16S rRNA from M. tuberculosis or a Mycobacterium other than tuberculosis (MOTT) species. In another embodiment, the amplifying step amplifies 16S rRNA or DNA encoding 16S rRNA from M. abscessus, M. africanum, M. asiaticum, M. avium, M. bovis, M. celatum, M. chelonae, M. flavescens, M. fortuitum, M. gastri, M. gordonae, M. haemophilum, M. intracellulare, M. interjectum, M. intermedium, M. kansasii, M. malmoense, M. marinum, M. non-chromogenicum, M. paratuberculosis, M. phlei, M. scrofulaceum, M. shimodei, M. simiae, M. smegmatis, M. szulgai, M. terrae, M. triviale, M. tuberculosis, M. ulcerans or M. xenopi. One embodiment, in the detecting step, uses at least one probe that hybridizes specifically to the amplified Mycobacterium nucleic acid. In a preferred embodiment, the detecting step uses at least one labeled probe that hybridizes specifically to the amplified Mycobacterium nucleic acid. In another preferred embodiment, the detecting step uses a plurality of probes that hybridize specifically to the amplified Mycobacterium nucleic acid. Embodiments of the method, in the amplifying step, use a combination of at least a first primer and a second primer, wherein the first primer is selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:12, and the second primer is selected from the group consisting of SEQ ID NO:13 to SEQ ID NO:34, SEQ ID NO:37 and SEQ ID NO:38. Some embodiments, in the amplifying step, use a combination of at least a first primer and a second primer, wherein the first primer is selected from the group consisting of SEQ ID NO:7 to SEQ ID NO:12, and the second primer is selected from the group consisting of SEQ ID NO:13 to SEQ ID NO:34, SEQ ID NO:37 and SEQ ID NO:38. Preferred embodiments of the method use, in the amplifying step, a combination of at least a first primer and a second primer selected from the group consisting of: the first primer having the sequence of SEQ ID NO:7, and the second primer having the sequence of SEQ ID NO:13; the first primer having the sequence of SEQ ID NO:7, and the second primer having the sequence of SEQ ID NO:14; the first primer having the sequence of SEQ ID NO:7, and the second primer having the sequence of SEQ ID NO:15; the first primer having the sequence of SEQ ID NO:7, and the second primer having the sequence of SEQ ID NO:16; the first primer having the sequence of SEQ ID NO:8, and the second primer having the sequence of SEQ ID NO:13; the first primer having the sequence of SEQ ID NO:8, and the second primer having the sequence of SEQ ID NO:14; the first primer having the sequence of SEQ ID NO:8, and the second primer having the sequence of SEQ ID NO:15; the first primer having the sequence of SEQ ID NO:9, and the second primer having the sequence of SEQ ID NO:13; the first primer having the sequence of SEQ ID NO:9, and the second primer having the sequence of SEQ ID NO:14; the first primer having the sequence of SEQ ID NO:9, and the second primer having the sequence of SEQ ID NO:15; the first primer having the sequence of SEQ ID NO:19, and the second primer having the sequence of SEQ ID NO:16; the first primer having the sequence of SEQ ID NO:11, and the second primer having the sequence of SEQ ID NO:13; the first primer having the sequence of SEQ ID NO:11, and the second primer having the sequence of SEQ ID NO:16; the first primer having the sequence of SEQ ID NO:11, and the second primer having the sequence of SEQ ID NO:17; the first primer having the sequence of SEQ ID NO:11, and the second primer having the sequence of SEQ ID NO:18; the first primer having the sequence of SEQ ID NO:11, and the second primer having the sequence of SEQ ID NO:19; the first primer having the sequence of SEQ ID NO:11, and the second primer having the sequence of SEQ ID NO:20; and the first primer having the sequence of SEQ ID NO:12, and the second primer having the sequence of SEQ ID NO:15. One embodiment, in the amplifying step, uses a combination of the first primer having the sequence of SEQ ID NO:11, and the second primer having the sequence of SEQ ID NO:16, SEQ ID NO:30 or SEQ ID NO:37. Another embodiment, in the amplifying step, uses a combination of the first primer having the sequence of SEQ ID NO:11, and two second primers having the sequences SEQ ID NO:16 and SEQ ID NO:37.
Another aspect of the invention is a composition for amplifying in an in vitro amplification reaction a Mycobacterium 16S rRNA sequence or DNA encoding 16S rRNA, comprising one or more oligonucleotides having a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO: 34, SEQ ID NO:37 and SEQ ID NO:38. One embodiment of the composition comprises at least one first oligonucleotide having the sequence of any one of SEQ ID NO:1 to SEQ ID NO:12, and at least one second oligonucleotide having the sequence of any one of SEQ ID NO:13 to SEQ ID NO:34, SEQ ID NO:37 or SEQ ID NO:38. Another embodiment comprises at least one first oligonucleotide containing the sequence of any one of SEQ ID NO:7 to SEQ ID NO:12, and at least one second oligonucleotide containing the sequence of any one of SEQ ID NO:13 to SEQ ID NO:34, SEQ ID NO:37 or SEQ ID NO:38.
Another aspect of the invention is a kit containing one or more oligonucleotides having a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:34, SEQ ID NO:37 and SEQ ID NO:38. In one embodiment, the kit contains at least one first oligonucleotide having the sequence of any one of SEQ ID NO:1 to SEQ ID NO:12, and at least one second oligonucleotide having the sequence of any one of SEQ ID NO:13 to SEQ ID NO:34, SEQ ID NO:37 or SEQ ID NO:38. Another embodiment of the kit contains at least one first oligonucleotide containing the sequence of any one of SEQ ID NO:7 to SEQ ID NO:12, and at least one second oligonucleotide containing the sequence of any one of SEQ ID NO:13 to SEQ ID NO:34, SEQ ID NO:37 or SEQ ID NO:38.
The present invention includes methods of detecting Mycobacterium nucleic acids, specifically 16S rRNA sequences, present in biological samples derived from humans, preferably in processed sputum samples. The present invention also includes compositions which include nucleic acid oligomers (xe2x80x9ccapture oligonucleotidesxe2x80x9d) used to specifically capture Mycobacterium 16S rRNA sequences present in a biological sample, amplification nucleic acid oligomers (xe2x80x9cprimersxe2x80x9d) used to specifically amplify selected portions of the captured 16S rRNA sequences and nucleic acid oligomers (xe2x80x9cprobesxe2x80x9d or xe2x80x9clabeled probesxe2x80x9d) for detecting amplified Mycobacterium sequences.
The nucleic acid sequences of this invention are useful for capturing, amplifying and detecting Mycobacterium nucleic acid present in a biological sample containing any of a variety of Mycobacterium species. The methods of the present invention are valuable for detecting Mycobacterium nucleic acid in a biological sample, and thus are important for diagnosis of infection that might result from a number of Mycobacterium species. These methods are especially important for screening for opportunistic infections by MOTT species or M. tuberculosis infections.
To aid in understanding terms used in describing the invention, the following definitions are provided.
By xe2x80x9cbiological samplexe2x80x9d is meant any tissue or material derived from a living or dead human which may contain Mycobacterium nucleic acid. Samples include, for example, sputum, respiratory tissue or exudates, peripheral blood, plasma or serum, cervical swab samples, biopsy tissue, gastrointestinal tissue, urine, feces, semen or other body fluids, tissues or materials. Samples also include bacterial cultures (liquid or on a solid media) and environmental samples. The biological sample may be treated to physically disrupt tissue or cell structure, thus releasing intracellular components into a solution which may further contain enzymes, buffers, salts, detergents and the like which are used to prepare the sample for analysis.
By xe2x80x9cnucleic acidxe2x80x9d is meant a multimeric compound comprising nucleosides or nucleoside analogs which have nitrogenous heterocyclic bases, or base analogs, where the nucleosides are covalently linked via a backbone structure to form a polynucleotide. Conventional ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) are included in the term xe2x80x9cnucleic acidxe2x80x9d as are analogs thereof. A nucleic acid backbone may comprise a variety of linkages known in the art, including one or more of sugar-phosphodiester linkages, peptide-nucleic acid bonds (referred to as xe2x80x9cpeptide nucleic acidsxe2x80x9d; Hydig-Hielsen et al., PCT Int""l Pub. No. WO 95/32305), phosphorothioate linkages, methylphosphonate linkages or combinations thereof. Sugar moieties of the nucleic acid may be either ribose or deoxyribose, or similar compounds having known substitutions, e.g., 2xe2x80x2 methoxy substitutions and/or 2xe2x80x2 halide substitutions. Nitrogenous bases may be conventional bases (A, G, C, T, U), known analogs thereof (e.g., inosine or others; see The Biochemistry of the Nucleic Acids 5-36, Adams et al., ed., 11th ed., 1992), or known derivatives of purine or pyrimidine bases (see, Cook, PCT Int""l Pub. No. WO 93/13121) and xe2x80x9cabasicxe2x80x9d residues in which the backbone includes no nitrogenous base for one or more residues (Arnold et al., U.S. Pat. No. 5,585,481). A nucleic acid may comprise only conventional sugars, bases and linkages, as found in RNA and DNA, or may include both conventional components and substitutions (e.g., conventional bases linked via a methoxy backbone, or a nucleic acid including conventional bases and one or more base analogs).
By xe2x80x9coligonucleotidexe2x80x9d or xe2x80x9coligomerxe2x80x9d is meant a nucleic acid having generally less than 1,000 residues, including polymers in a size range having a lower limit of about 2 to 5 nucleotide residues and an upper limit of about 500 to 900 nucleotide residues. Preferred oligomers are in a size range having a lower limit of about 5 to about 15 residues and an upper limit of about 50 to 600 residues; more preferably, in a size range having a lower limit of about 10 residues and an upper limit of about 100 residues. Oligomers may be purified from naturally occurring sources, but preferably are synthesized using well known methods.
By xe2x80x9camplification oligonucleotidexe2x80x9d orxe2x80x9camplification oligomerxe2x80x9d is meant an oligonucleotide that hybridizes to a target nucleic acid, or its complement, and participates in an in vitro nucleic acid amplification reaction (e.g., primers and promoter-primers). Preferably, an amplification oligonucleotide contains at least about 10 contiguous bases, and more preferably at least about 12 contiguous bases, which are complementary to a region of the target nucleic acid sequence (or a complementary strand thereof). The contiguous bases are preferably at least 80%, and more preferably at least 90% complementary to the sequence to which the amplification oligonucleotide binds. An amplification oligonucleotide is preferably about 10 to about 60 bases long and may include modified nucleotides or base analogs.
Amplification oligonucleotides and oligomers may be referred to as xe2x80x9cprimersxe2x80x9d or xe2x80x9cpromoter-primers.xe2x80x9d A xe2x80x9cprimerxe2x80x9d refers to an oligonucleotide which is capable of hybridizing to a template nucleic acid and which has a 3xe2x80x2 end that is extended in a polymerization reaction, usually mediated by an enzyme. The 5xe2x80x2 region of the primer may be non-complementary to the target nucleic acid and include additional bases, such as a promoter sequence. Such a primer is referred to as a xe2x80x9cpromoter-primer.xe2x80x9d Those skilled in the art will appreciate that any oligomer that can function as a primer can be modified to include a 5xe2x80x2 promoter sequence, and thus could function as a promoter-primer. Similarly, any promoter-primer can serve as a primer, independent of its promoter sequence function.
By xe2x80x9camplificationxe2x80x9d is meant any known in vitro procedure for obtaining multiple copies of a target nucleic acid sequence or its complement or fragments thereof. In vitro amplification refers to production of an amplified nucleic acid that may contain less than the complete target region sequence or its complement. Known amplification methods include, e.g., transcription-mediated amplification, replicase-mediated amplification, polymerase chain reaction (PCR) amplification, ligase chain reaction (LCR) amplification and strand-displacement amplification (SDA). Replicase-mediated amplification uses self-replicating RNA molecules, and a replicase such as QB-replicase (Kramer et al., U.S. Pat. No. 4,786,600; PCT Int""l Pub. No. WO 90/14439). PCR amplification is well known and uses DNA polymerase, primers and thermal cycling to synthesize multiple copies of the two complementary strands of DNA or cDNA (Mullis et al., U.S. Pat. Nos. 4,683,195, 4,683,202, and 4,800,159; Methods in Enzymology, 1987, Vol. 155: 335-350). LCR amplification uses at least four separate oligonucleotides to amplify a target and its complementary strand by using multiple cycles of hybridization, ligation, and denaturation (EP Pat. App. Pub. No. 0 320 308). SDA is a method in which a primer contains a recognition site for a restriction endonuclease such that the endonuclease will nick one strand of a hemimodified DNA duplex that includes the target sequence, followed by amplification in a series of primer extension and strand displacement steps (Walker et al., 1992, Proc. Natl. Acad. Sci. USA 89:392-396; and U.S. Pat. No. 5,422,252). Transcription-mediated amplification is used in preferred embodiments of the present invention. Those skilled in the art will understand that the oligonucleotide primer sequences of the present invention may be readily used in any in vitro amplification method based on primer extension by a polymerase.
By xe2x80x9ctranscription-mediated amplificationxe2x80x9d or xe2x80x9ctranscription-associated amplificationxe2x80x9d is meant any type of nucleic acid amplification that uses an RNA polymerase to produce multiple RNA transcripts from a nucleic acid template. Transcription-mediated amplification (xe2x80x9cTMAxe2x80x9d) generally employs an RNA polymerase activity, a DNA polymerase activity, deoxyribonucleoside triphosphates, ribonucleoside triphosphates, and a promoter-primer and a second non-promoter primer, and optionally may include one or more additional oligonucleotides (sometimes referred to as xe2x80x9chelpersxe2x80x9d). Transcription-associated amplification methods are well known in the art, as disclosed in detail elsewhere (Kacian et al, U.S. Pat. Nos. 5,399,491 and 5,554,516; Kacian et al., PCT Int""l Pub. No. WO 93/22461; Burg et al., U.S. Pat. No. 5,437,990; Gingeras et al., PCT Int""l Pub. Nos. WO 88/01302 and WO 88/10315; Malek et al, U.S. Pat. No. 5,130,238; Urdea et al., U.S. Pat. Nos. 4,868,105 and 5,124,246; McDonough et al., PCT Int""l Pub. No. WO 94/03472; and Ryder et al., PCT Int""l Pub. No. WO 95/03430). Preferred transcription-mediated amplification methods used in embodiments of the present invention are those disclosed by Kacian et al. (U.S. Pat. Nos. 5,399,491 and 5,554,516; PCT Application No. WO 93/22461).
By xe2x80x9cprobexe2x80x9d is meant a nucleic acid oligomer that hybridizes specifically to a target sequence in a nucleic acid or its complement, preferably in an amplified nucleic acid, under conditions that promote hybridization, thereby allowing detection of the target sequence or amplified nucleic acid. Detection may either be direct (i.e., resulting from a probe hybridizing directly to the target sequence or amplified nucleic acid) or indirect (i.e., resulting from a probe hybridizing to an intermediate molecular structure that links the probe to the target sequence or amplified nucleic acid). A probe""s xe2x80x9ctargetxe2x80x9d generally refers to a sequence within (i.e., a subset of) an amplified nucleic acid sequence which hybridizes specifically to at least a portion of a probe oligomer using standard hydrogen bonding (i.e., base pairing). Sequences that are xe2x80x9csufficiently complementaryxe2x80x9d allow stable hybridization of a probe oligomer to a target sequence, even if the two sequences are not completely complementary. A probe may be labeled or unlabeled, depending on the method of detection used.
By xe2x80x9csufficiently complementaryxe2x80x9d is meant a contiguous nucleic acid base sequence that is capable of hybridizing to another base sequence by hydrogen bonding between a series of complementary bases. Complementary base sequences may be complementary at each position in sequence using standard base pairing (e.g., G:C, A:T or A:U pairing) or may contain one or more residues that are not complementary using standard hydrogen bonding (including abasic residues), but in which the entire complementary base sequence is capable of specifically hybridizing with another base sequence in appropriate hybridization conditions. Contiguous bases are preferably at least about 80%, more preferably at least about 90% complementary to a sequence to which an oligomer specifically hybridizes. Appropriate hybridization conditions are well known to those skilled in the art, can be predicted readily based on sequence composition and conditions, or can be determined empirically by using routine testing (see Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989) at xc2xa7xc2xa71.90-1.91, 7.37-7.57, 9.47-9.51 and 11.47-11.57, particularly at xc2xa7xc2xa79.50-9.51, 11.12-11.13, 11.45-11.47 and 11.55-11.57).
By xe2x80x9ccapture oligonucleotidexe2x80x9d or xe2x80x9ccapture oligomerxe2x80x9d is meant at least one nucleic acid oligomer that provides means for specifically joining a target sequence and an immobilized oligomer based on base pair hybridization (see PCT Application WO 98/50583). Generally, a capture oligomer includes two binding regions: a target-specific binding region and an immobilized probe-specific binding region Sometimes, a capture oligomer is referred to as a xe2x80x9ccapture probe.xe2x80x9d
By xe2x80x9cimmobilized probexe2x80x9d or xe2x80x9cimmobilized nucleic acidxe2x80x9d is meant a nucleic acid that joins, directly or indirectly, a capture oligomer to a solid support. An immobilized probe is an oligomer joined to a solid support that facilitates separation of bound target sequence from unbound material in a sample. Any known solid support may be used, such as matrices and particles free in solution, made of any known material (e.g., nitrocellulose, nylon, glass, polyacrylate, mixed polymers, polystyrene, silane polypropylene and metal particles, preferably paramagnetic particles). Preferred supports are monodisperse paramagnetic spheres (i.e., uniform in sizexc2x1about 5%), thereby providing consistent results, to which an immobilized probe is stably joined directly (e.g., via a direct covalent linkage, chelation, or ionic interaction), or indirectly (e.g., via one or more linkers), permitting hybridization to another nucleic acid in solution.
By xe2x80x9cseparatingxe2x80x9d or xe2x80x9cpurifyingxe2x80x9d is meant that one or more components of the biological sample are removed from one or more other components of the sample. Sample components include nucleic acids in a generally aqueous solution which may also include other materials (e.g., proteins, carbohydrates, lipids and/or nucleic acids). Preferably, a separating or purifying step removes at least about 70%, more preferably at least about 90% and, even more preferably, at least about 95% of the other components present in the sample.
By xe2x80x9clabelxe2x80x9d is meant a molecular moiety or compound that can be detected or can lead to a detectable response. A label is joined, directly or indirectly, to a nucleic acid probe or to the nucleic acid to be detected (e.g., amplified product). Direct labeling can occur through bonds or interactions that link the label to the probe (e.g., covalent bonds or non-covalent interactions). Indirect labeling can occur through use of a bridging moiety or xe2x80x9clinkerxe2x80x9d such as additional oligonucleotide(s), which is either directly or indirectly labeled. Bridging moieties can be used to amplify a detectable signal. Labels can be any known detectable moiety (e.g., a radionuclide, ligand such as biotin or avidin, enzyme or enzyme substrate, reactive group, or chromophore, such as a dye or colored particle, luminescent compond, including bioluminescent, phosphorescent or chemiluminescent compounds, and fluorescent compound). Preferably, the label on a labeled probe that is detectable in a homogeneous assay system (i.e., in a mixture, bound labeled probe exhibits a detectable change compared to unbound labeled probe). A preferred label for use in a homogenous assay is a chemiluminescent compound (see U.S. Pat. Nos. 5,656,207, 5,658,737 and 5,639,604), more preferably an acridinium ester (xe2x80x9cAExe2x80x9d) compound, such as standard AE or derivatives thereof. Methods of attaching labels to nucleic acids and detecting labels are well known in the art (e.g., see Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd ed. (Cold Spring Harbor Laboratory Press, Cold Spring Habor, N.Y., 1989), Chapt. 10; U.S. Pat. Nos. 5,658,737, 5,656,207, 5,547,842, 5,283,174 and 4,581,333; and European Pat. App. No. 0 747 706).
A xe2x80x9chomogeneous detectable labelxe2x80x9d refers to a label whose presence can be detected in a homogeneous fashion based upon whether the label is on a probe hybridized to a target sequence. That is, a homogeneous detectable label can be detected without physically removing hybridized from unhybridized forms of the label or labeled probe. Homogeneous detectable labels and methods of detecting them have been previously described in detail (U.S. Pat. Nos. 5,283,174, 5,656,207 and 5,658,737).
By xe2x80x9cconsisting essentially ofxe2x80x9d is meant that additional component(s), composition(s) or method step(s) that do not materially change the basic and novel characteristics of the present invention may be included in the compositions or kits or methods of the present invention. Such characteristics include the ability to detect Mycobacterium species rRNA sequences and/or DNA sequences encoding the rRNA in a biological sample at a copy number of about 100 or more per sample. Any component(s), composition(s), or method step(s) that have a material effect on the basic characteristics of the present invention would fall outside of this term.
Unless defined otherwise, all scientific and technical terms used herein have the same meaning as commonly understood by those skilled in the relevant art. General definitions of many of the terms used herein are provided, for example, in Dictionary of Microbiology and Molecular Biology, 2nd ed. (Singleton et al., 1994, John Wiley and Sons, New York, N.Y.) or The Harper Collins Dictionary of Biology (Hale and Marham, 1991, Harper Perennial, New York, N.Y.). Unless mentioned otherwise, the techniques employed or contemplated herein are standard methodologies well known to one of ordinary skill in the art.
The present invention includes compositions (nucleic acid capture oligomers, amplification oligomers and probes) and methods for detecting Mycobacterium species nucleic acid in a human biological sample. To select DNA sequences appropriate for use as capture oligomers, primers and probes, known rRNA or the corresponding genomic sequences from M. tuberculosis, and MOTT species, such as M. celatum and M. xenopi, including partial or complementary sequences, available from publicly accessible databases (e.g., GenBank) were aligned by matching regions of the same or similar sequences and compared using well known molecular biology techniques. Although sequence comparisons may be facilitated by using algorithms, those skilled in the art can readily perform such comparisons manually. Portions of sequences containing relatively few sequence variants between the compared sequences were chosen as a basis for designing synthetic oligomers suitable for use in capture, amplification and detection of amplified sequences. Other considerations in designing oligomers included the relative GC content of the sequence (ranging from about 30-55%) and the relative absence of predicted secondary structure (e.g., hairpin structures) within a sequence, all well known in the art. Based on these analyses, the oligomers having sequences of SEQ ID NO:1 to SEQ ID NO:35 were designed and synthesized.
Target capture is preferably included in the method to increase the concentration or purity of the target nucleic acid before in vitro amplification. Preferably, target capture involves a relatively simple method of hybridizing and isolating the target nucleic acid, as described in detail in PCT WO 98/50583. Briefly, an oligonucleotide attached to a solid support is put in contact with a mixture containing the target nucleic acid under appropriate hybridization conditions to allow the target nucleic acid to be releasably attached to the solid support. Target capture may result from direct hybridization between the target nucleic acid and the oligonucleotide attached to the solid support, or may be indirectly with one or more oligonucleotides forming a hybridization complex that links the target nucleic acid to the oligonucleotide attached to the solid support. The solid support is preferably a particle that can be readily separated from the solution, more preferably a paramagnetic particle that can be retrieved by applying a magnetic field to the vessel. Then, the target nucleic acid linked to the solid support is washed and amplified upon exposure to the appropriate primers, substrates and enzymes in an in vitro amplification reaction.
Generally, for capture oligomer sequences, the oligomer includes a sequence that specifically binds to the target sequence and a xe2x80x9ctailxe2x80x9d sequence used in capturing the complex to an immobilized sequence (e.g., T14 oligomer) on the solid support. That is, the capture oligomer includes a sequence that binds specifically to Mycobacterium rRNA sequence which is covalently attached to a 3xe2x80x2 tail sequence (e.g., a poly-A sequence complementary to the immobilized sequence). Any backbone to linking the base sequence of a capture oligomer may be used, but preferably the capture oligomer backbone includes O-methoxy linkages. The tail sequence (preferably 5-50 nt long) hybridizes to an immobilized complementary sequence to purify the hybridized target nucleic acid from the other sample components. A preferred capture oligomer has the sequence of SEQ ID NO:35 (CTAGTCTGCCCGTTTT(A)30).
Amplifying the captured target region using at least two primers can be accomplished using a variety of known nucleic acid amplification reactions, but preferably uses a transcription-associated amplification reaction. Using such an in vitro amplification method, many strands of nucleic acid are produced from a single copy of target nucleic acid, thus permitting detection of the target by specifically binding the amplified sequences to one or more detecting probes. Transcription-associated amplification has been described in detail elsewhere (Kacian et al., U.S. Pat. Nos. 5,399,491 and 5,554,516). Preferably, transcription-associated amplification uses two types of primers (one referred to as a promoter-primer because it contains a promoter sequence for an RNA polymerase), two enzymes (a reverse transcriptase (RT) and an RNA polymerase), substrates (deoxyribonucleoside triphosphates, ribonucleoside triphosphates) and appropriate salts and buffers in solution to produce multiple RNA transcripts from a nucleic acid template. Briefly, in the first step, a promoter-primer hybridizes specifically to a target RNA sequence and reverse transcriptase creates a first strand cDNA by extension from the 3xe2x80x2 end of the promoter-primer. Making the cDNA available for hybridization with the second primer may be achieved by using techniques well known in the art, such as, by denaturing the duplex or using RNase H activity. Preferably, RNase H activity supplied by the reverse transcriptase degrades the RNA in the resulting DNA:RNA duplex. A second primer then binds to the cDNA and a new strand of DNA is synthesized from the end of the second primer using the reverse transcriptase, to create a double-stranded DNA having a functional promoter sequence at one end. The RNA polymerase binds to the double-stranded promoter sequence and transcription produces multiple transcripts or xe2x80x9camplicons.xe2x80x9d These amplicons then are used in the transcription-associated amplification process, each serving as a template for a new round of replication, thus generating large amounts of single-stranded amplified nucleic acid (about 100 to about 3,000 copies of RNA transcripts synthesized from a single template). Preferably, amplification uses substantially constant reaction conditions (i.e., is substantially isothermal).
Primer sequences (SEQ ID NO:1 to SEQ ID NO:34, SEQ ID NO:37) bind specifically to a target sequence or a complement of a target sequence, although primer sequences may contain sequences that do not bind to the target sequence or its complement. In particular, T7 promoter-primers (SEQ ID NO:7 to SEQ ID NO:12) include a T7 promoter sequence (shown separately in SEQ ID NO:36) attached to the portion of the primer sequence that binds to the target or its complement. Those skilled in the art will appreciate that a target-specific primer sequence, with or without an attached promoter sequence (SEQ ID NO:1 to SEQ ID NO:6), may be used as a primer in a variety of in vitro amplification conditions.
Preferred methods of the present invention are described in the examples that follow. Briefly, the assays include the steps of providing a biological sample containing the target Mycobacterium rRNA, target capture of the rRNA, in vitro nucleic acid amplification and detection of the amplified nucleic acid products. In preferred embodiments that use transcription-mediated amplification (TMA), the final amplification mixture includes the captured target rRNA, at least one T7 promoter-primer that includes a target-specific sequence and a T7 promoter sequence, at least one second (non-T7) primer that hybridizes specifically to a first strand cDNA made from the target using the T7 promoter-primer, and substrates and cofactors for enzymatic polymerization by reverse transcriptase and T7 RNA polymerase in the mixture. The captured target rRNA does not have to be separated from the solid support for use in the TMA reaction. The T7 promoter sequence, when double-stranded, serves as a functional promoter for T7 RNA polymerase to produce multiple transcripts. The amplified products may be detected using any of a variety of known methods, including hybridizing the amplified products, or portions thereof, to a complementary probe sequence. The probe which includes a sequence that hybridizes specifically to a portion of the target region that is amplified using the two amplification oligonucleotides. In some embodiments, a labeled probe is used to detect the amplified products, whereas in other embodiments, the amplified products are labeled and hybridized to immobilized probes, preferably many probes present in an array. The complex of the probe and the hybridized amplified product is then detected.
More specifically, a typical assay used the following steps and conditions. A sample (e.g., 0.5 ml of sputum sediment or bacterial culture, and for positive control reactions, an equal volume of water or buffer containing a known amount of rRNA) was mixed with an equal volume of a 2xc3x97lysis buffer (e.g., 20 mM HEPES, 0.5% (w/v) lithium lauryl sulfate, pH 8) in a tube. To release nucleic acids from the bacteria, the mixture was vortexed in the presence of glass beads, or sonicated for 15 min, and unlysed organisms were heat killed by incubating at 95xc2x0 C. for 15 min.
Generally 250 xcexcl of the lysate was used in the target capture step in a new tube. To capture the target rRNA, the mixture included 250 xcexcl of prepared sample, 250 xcexcl of a target capture solution containing 5 pmols of SEQ ID NO:35, and 50 xcexcg of paramagnetic particles (0.7-1.05xcexc particles, Seradyn, Indianapolis, Ind.) with attached immobilized poly-dT14 probe. Immobilized probes were attached using standard carbodiimide chemistry methods (Lund, et al., 1988, Nuc. Acids Res. 16:10861-10880). The target capture mixture was heated at 60xc2x0 C. for about 20 min and then cooled to room temperature to allow hybridization. A magnetic field was applied for 5 min to attract the magnetic particles with the attached complex containing the target RNA to a location on the reaction container (substantially as described in U.S. Pat. No. 4,895,650). The particles were then washed twice with 1 ml of a washing buffer (10 mM HEPES, 6.5 mM NaOH, 1 mM EDTA, 150 mM NaCl, 0.1% (w/v) sodium lauryl sulfate) by resuspending the particles in the buffer and repeating the magnetic separation step.
For transcription mediated amplification, performed substantially as described previously (Kacian et al., U.S. Pat. Nos. 5,399,491 and 5,554,516), washed particles were suspended in 75 xcexcl of amplification reagent solution (1.1 mM rUTP, 4 mM rATP, 2.7 mM rCTP, 6.7 mM rGTP, 0.67 mM each dNTP, 13.3 mM KCl, 47 mM Tris, 17.1 mM MgCl) and at least two primer oligomers (at least one promoter-primer and a second primer, usually at 0.08 xcexcM final concentration), and covered with a layer (200 xcexcl) of inert oil to prevent evaporation. The mixture was incubated at 42xc2x0 C. for 5 min, and then 25 xcexcl of enzyme reagent was added (containing 2800 U of MMLV RT and 2000 U of T7 RNA polymerase per reaction, in a buffer containing 50 mM HEPES, 1 mM EDTA, 10% (v/v) Triton(trademark) X-100, 120 mM KCl, 20% (v/v) glycerol). The mixture was shaken gently and further incubated at 42xc2x0 C. for 1 hr. Negative controls consisted of all of the same reagents but substituting for target an equal volume of water or buffer that contained no target nucleic acid.
Amplified Mycobacterium sequences were detected, in some cases, using an acridinium ester (AE)-labeled probe which was detected by chemiluminescence in a suitable luminometer (e.g., LEADER(trademark) luminometer, Gen-Probe Incorporated, San Diego, Calif.) and expressed in relative light units (RLU) substantially as described previously (U.S. Pat. No. 5,658,737 at column 25, lines 27-46; Nelson et al., 1996, Biochem. 35:8429-8438 at 8432). Generally, the average (mean) of detected RLU for replicate assays are reported. The probes were: for M. tuberculosis detection, SEQ ID NO:39 (GTCTTGTGGTGGAAAGCGCMAG), for M. avium detection, SEQ ID NO:40 (GGACCTCAAGACGCATGTC), for M. xenopi detection, SEQ ID NO:41 (TAGGACCATTCTGCGCATGTG), and for M. gastri and M. Kansasii, SEQ ID NO:42 (TAGGACCACTTGGCGCATGCC).
In other cases, the amplified sequences were detected on an immobilized array of DNA probes specific for detection of Mycobacterium sequences, as described in detail previously (A. Troesch et al, 1999, J. Clin. Microbiol. 37(1): 49-55). The analysis was performed on the GeneChip(trademark) instrumentation system (Affymetrix, Santa Clara, Calif.) to detect the intensity and pattern of fluorescent signals (expressed as relative fluorescence units or RFU) on the hybridized array. Briefly, this system comprises a GeneChip(trademark) fluidics station, GeneArray(trademark) scanner (Hewlett-Packard, Palo Alto, Calif.) and GeneChip(trademark) analysis software, an algorithm to determine nucleotide base calling and determine the nucleic acid sequence present in the amplified nucleic acid. The system reports the most likely Mycobacterium species present.
The following non-limiting examples demonstrate aspects of preferred embodiments of the present invention.